COVID-19 outbreaks among crew on commercial ships at the Port of Rotterdam, the Netherlands, 2020 to 2021.

BackgroundDuring the COVID-19 pandemic, international shipping activity was disrupted as movement of people and goods was restricted. The Port of Rotterdam, the largest port in Europe, remained operational throughout.AimWe describe the burden of COVID-19 among crew on sea-going vessels at the port and recommend improvements in future infectious disease event notification and response at commercial ports.MethodsSuspected COVID-19 cases on sea-going vessels were notified to port authorities and public health (PH) authorities pre-arrival via the Maritime Declaration of Health. We linked data from port and PH information systems between 1 January 2020 and 31 July 2021, derived a notification rate (NR) of COVID-19 events per arrival, and an attack rate (AR) per vessel (confirmed cases). We compared AR by vessel type (workship/tanker/cargo/passenger), during wildtype-, alpha- and delta-dominant calendar periods.ResultsEighty-four COVID-19 events were notified on ships, involving 622 cases. The NR among 45,030 new arrivals was 173 per 100,000 impacting 1% of vessels. Events per week peaked in April 2021 and again in July 2021, when the AR was also highest. Half of all cases were notified on workships, events occurring earlier and more frequently than on other vessels.ConclusionNotification of COVID-19 events on ships occurred infrequently, although case under-ascertainment was likely. Pre-agreed protocols for data-sharing between stakeholders locally and across Europe would facilitate more efficient pandemic response. Public health access to specimens for sequencing and environmental sampling would give greater insight into viral spread on ships.

Capturing the SARS-CoV-2 infection pyramid within the municipality of Rotterdam using longitudinal sewage surveillance.

Despite high vaccination rates in the Netherlands, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to circulate. Longitudinal sewage surveillance was implemented along with the notification of cases as two parts of the surveillance pyramid to validate the use of sewage for surveillance, as an early warning tool, and to measure the effect of interventions. Sewage samples were collected from nine neighborhoods between September 2020 and November 2021. Comparative analysis and modeling were performed to understand the correlation between wastewater and case trends. Using high resolution sampling, normalization of wastewater SARS-CoV-2 concentrations, and 'normalization' of reported positive tests for testing delay and intensity, the incidence of reported positive tests could be modeled based on sewage data, and trends in both surveillance systems coincided. The high collinearity implied that high levels of viral shedding around the onset of disease largely determined SARS-CoV-2 levels in wastewater, and that the observed relationship was independent of variants of concern and vaccination levels. Sewage surveillance alongside a large-scale testing effort where 58 % of a municipality was tested, indicated a five-fold difference in the number of SARS-CoV-2-positive individuals and reported cases through standard testing. Where trends in reported positive cases were biased due to testing delay and testing behavior, wastewater surveillance can objectively display SARS-CoV-2 dynamics for both small and large locations and is sensitive enough to measure small variations in the number of infected individuals within or between neighborhoods. With the transition to a post-acute phase of the pandemic, sewage surveillance can help to keep track of re-emergence, but continued validation studies are needed to assess the predictive value of sewage surveillance with new variants. Our findings and model aid in interpreting SARS-CoV-2 surveillance data for public health decision-making and show its potential as one of the pillars of future surveillance of (re)emerging viruses.

Rise and fall of SARS-CoV-2 variants in Rotterdam: Comparison of wastewater and clinical surveillance.

Monitoring of SARS-CoV-2 in wastewater (WW) is a promising tool for epidemiological surveillance, correlating not only viral RNA levels with the infection dynamics within the population, but also to viral diversity. However, the complex mixture of viral lineages in WW samples makes tracking of specific variants or lineages circulating in the population a challenging task. We sequenced sewage samples of 9 WW-catchment areas within the city of Rotterdam, used specific signature mutations from individual SARS-CoV-2 lineages to estimate their relative abundances in WW and compared them against those observed in clinical genomic surveillance of infected individuals between September 2020 and December 2021. We showed that especially for dominant lineages, the median of the frequencies of signature mutations coincides with the occurrence of those lineages in Rotterdam's clinical genomic surveillance. This, along with digital droplet RT-PCR targeting signature mutations of specific variants of concern (VOCs), showed that several VOCs emerged, became dominant and were replaced by the next VOC in Rotterdam at different time points during the study. In addition, single nucleotide variant (SNV) analysis provided evidence that spatio-temporal clusters can also be discerned from WW samples. We were able to detect specific SNVs in sewage, including one resulting in the Q183H amino acid change in the Spike gene, that was not captured by clinical genomic surveillance. Our results highlight the potential use of WW samples for genomic surveillance, increasing the set of epidemiological tools to monitor SARS-CoV-2 diversity.

Normalisation of SARS-CoV-2 concentrations in wastewater: The use of flow, electrical conductivity and crAssphage.

Over the course of the Corona Virus Disease-19 (COVID-19) pandemic in 2020-2022, monitoring of the severe acute respiratory syndrome coronavirus 2 ribonucleic acid (SARS-CoV-2 RNA) in wastewater has rapidly evolved into a supplementary surveillance instrument for public health. Short term trends (2 weeks) are used as a basis for policy and decision making on measures for dealing with the pandemic. Normalisation is required to account for the dilution rate of the domestic wastewater that can strongly vary due to time- and location-dependent sewer inflow of runoff, industrial discharges and extraneous waters. The standard approach in sewage surveillance is normalisation using flow measurements, although flow based normalisation is not effective in case the wastewater volume sampled does not match the wastewater volume produced. In this paper, two alternative normalisation methods, using electrical conductivity and crAssphage have been studied and compared with the standard approach using flow measurements. For this, a total of 1116 24-h flow-proportional samples have been collected between September 2020 and August 2021 at nine monitoring locations. In addition, 221 stool samples have been analysed to determine the daily crAssphage load per person. Results show that, although crAssphage shedding rates per person vary greatly, on a population-level crAssphage loads per person per day were constant over time and similar for all catchments. Consequently, crAssphage can be used as a quantitative biomarker for populations above 5595 persons. Electrical conductivity is particularly suitable to determine dilution rates relative to dry weather flow concentrations. The overall conclusion is that flow normalisation is necessary to reliably determine short-term trends in virus circulation, and can be enhanced using crAssphage and/or electrical conductivity measurement as a quality check.

COVID on the Seas: SARS-CoV-2 in Commercial Shipping, Port of Rotterdam, The Netherlands, 2020-2021

We analysed all proven cases of SARS-CoV-2 on sea-going vessels entering or present in the Port of Rotterdam to illustrate the burden of the corona pandemic on commercial shipping. We calculated the notification rate (NR) per arrival and attack rate per vessel and correlated outbreak sizes by vessel type over time during the pandemic using routinely gathered data from the port and public health (PH) authorities.

COVID-19 vaccine effectiveness against SARS-CoV-2 infection during the Delta period, a nationwide study adjusting for chance of exposure, the Netherlands, July to December 2021.

BackgroundDifferential SARS-CoV-2 exposure between vaccinated and unvaccinated individuals may confound vaccine effectiveness (VE) estimates.AimWe conducted a test-negative case-control study to determine VE against SARS-CoV-2 infection and the presence of confounding by SARS-CoV-2 exposure.MethodsWe included adults tested for SARS-CoV-2 at community facilities between 4 July and 8 December 2021 (circulation period of the Delta variant). The VE against SARS-CoV-2 infection after primary vaccination with an mRNA (Comirnaty or Spikevax) or vector-based vaccine (Vaxzevria or Janssen) was calculated using logistic regression adjusting for age, sex and calendar week (Model 1). We additionally adjusted for comorbidity and education level (Model 2) and SARS-CoV-2 exposure (number of close contacts, visiting busy locations, household size, face mask wearing, contact with SARS-CoV-2 case; Model 3). We stratified by age, vaccine type and time since vaccination.ResultsVE against infection (Model 3) was 64% (95% CI: 50-73), only slightly lower than in Models 1 (68%; 95% CI: 58-76) and 2 (67%; 95% CI: 56-75). Estimates stratified by age group, vaccine and time since vaccination remained similar: mRNA VE (Model 3) among people ≥ 50 years decreased significantly (p = 0.01) from 81% (95% CI: 66-91) at < 120 days to 61% (95% CI: 22-80) at ≥ 120 days after vaccination. It decreased from 83% to 59% in Model 1 and from 81% to 56% in Model 2.ConclusionSARS-CoV-2 exposure did not majorly confound the estimated COVID-19 VE against infection, suggesting that VE can be estimated accurately using routinely collected data without exposure information.

Population-based screening in a municipality after a primary school outbreak of the SARS-CoV-2 Alpha variant, the Netherlands, December 2020-February 2021.

An outbreak of SARS-CoV-2 Alpha variant (Pango lineage B.1.1.7) was detected at a primary school (School X) in Lansingerland, the Netherlands, in December 2020. The outbreak was studied retrospectively, and population-based screening was used to assess the extent of virus circulation and decelerate transmission. Cases were SARS-CoV-2 laboratory confirmed and were residents of Lansingerland (November 16th 2020 until February 22th 2021), or had an epidemiological link with School X or neighbouring schools. The SARS-CoV-2 variant was determined using variant PCR or whole genome sequencing. A questionnaire primarily assessed clinical symptoms. A total of 77 Alpha variant cases were found with an epidemiological link to School X, 16 Alpha variant cases linked to the neighbouring schools, and 146 Alpha variant cases among residents of Lansingerland without a link to the schools. The mean number of self-reported symptoms was not significantly different among Alpha variant infected individuals compared to non-Alpha infected individuals. The secondary attack rate (SAR) among Alpha variant exposed individuals in households was 52% higher compared to non-Alpha variant exposed individuals (p = 0.010), with the mean household age, and mean number of children and adults per household as confounders. Sequence analysis of 60 Alpha variant sequences obtained from cases confirmed virus transmission between School X and neighbouring schools, and showed that multiple introductions of the Alpha variant had already taken place in Lansingerland at the time of the study. The alpha variant caused a large outbreak at both locations of School X, and subsequently spread to neighbouring schools, and households. Population-based screening (together with other public health measures) nearly stopped transmission of the outbreak strain, but did not prevent variant replacement in the Lansingerland municipality.

Community-based SARS-CoV-2 testing in low-income neighbourhoods in Rotterdam: Results from a pilot study.

Background: High incidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and low testing uptake were reported in low-income neighbourhoods in Rotterdam. We aimed to improve willingness and access to testing by introducing community-based test facilities, and to evaluate the effectiveness of a rapid antigen detection test (RDT). Methods: Two to eleven test facilities operated consecutively in three low-income neighbourhoods in Rotterdam, offering the options of walk-in or appointments. Background characteristics were collected at intake and one nasopharyngeal swab was taken and processed using both RDT and reverse transcription polymerase chain reaction (RT-PCR). Visitors were asked to join a survey for evaluation purposes. Results: In total, 19 773 visitors were tested - 9662 (48.9%) without an appointment. Walk-in visitors were older, lived more often in the proximity of the test facilities, and reported coronavirus disease (COVID-19)-related symptoms less often than by-appointment visitors. For 67.7% of the visitors, this was the first time they got tested. A total of 1211 (6.1%) tested SARS-CoV-2-positive with RT-PCR, of whom 309 (25.5%) were asymptomatic. Test uptake increased among residents of the pilot neighbourhoods, especially in the older age groups, compared to people living in comparable neighbourhoods without community-based testing facilities. RDT detected asymptomatic individuals with 71.8% sensitivity, which was acceptable in this high prevalence setting. Visitors reported positive attitudes towards the test facilities and welcomed the easy access. Conclusions: Offering community-based SARS-CoV-2 testing seems a promising approach for increasing testing uptake among specific populations in low-income neighbourhoods.

Increasing incidence of reported scabies infestations in the Netherlands, 2011-2021.

INTRODUCTION: Several Public Health Services and general practitioners in the Netherlands observed an increase in scabies in the Netherlands. Since individual cases of scabies are not notifiable in the Netherlands, the epidemiological situation is mostly unknown. To investigate the scabies incidence in the Netherlands, we described the epidemiology of scabies between 2011 and 2021. METHODS: Two national data sources were analysed descriptively. One data source obtained incidence data of scabies (per 1,000 persons) of persons consulting in primary care from 2011-2020. The other data source captured the number of prescribed scabicides in the Netherlands from 2011-2021. To describe the correlation between the incidence of diagnoses and the number of dispensations between 2011 and 2020, we calculated a correlation coefficient. RESULTS: The incidence of reported scabies has increased by more than threefold the last decade (2011-2020), mainly affecting adolescents and (young) adults. This was also clearly reflected in the fivefold increase in dispensations of scabicide medication during 2011-2021. The incidence and dispensations were at an all-time high in 2021. We found a strong correlation between the reported incidence and the number of dispensations between 2011 and 2020. CONCLUSIONS: More awareness on early diagnosis, proper treatment and treatment of close contacts is needed.

A sharp decrease in reported non-COVID-19 notifiable infectious diseases during the first wave of the COVID-19 epidemic in the Rotterdam region, the Netherlands: a descriptive study.

BACKGROUND: The Public Health Services in the Rotterdam region, the Netherlands, observed a substantial decrease of non-COVID-19 notifiable infectious diseases and institutional outbreaks during the first wave of the COVID-19 epidemic. We describe this change from mid-March to mid-October 2020 by comparing with the pre-COVID-19 situation. METHODS: All cases of notifiable diseases and institutional outbreaks reported to the Public Health Services Rotterdam-Rijnmond between 1st January and mid-October 2020 were included. Seven-day moving averages and cumulative cases were plotted against time and compared to those of 2017-2019. Additionally, Google mobility transit data of the region were plotted, as proxy for social distancing. RESULTS: Respiratory, gastrointestinal, and travel-related notifiable diseases were reported 65% less often during the first wave of the COVID-19 epidemic than in the same weeks in 2017-2019. Reports of institutional outbreaks were also lower after the initially imposed social distancing measures; however, the numbers rebounded when measures were partially lifted. CONCLUSIONS: Interpersonal distancing and hygiene measures imposed nationally against COVID-19 were in place between mid-March and mid-October, which most likely reduced transmission of other infectious diseases, and may thus have resulted in lower notifications of infectious diseases and outbreaks. This phenomenon opens future study options considering the effect of local outbreak control measures on a wide range of non-COVID-19 diseases. Targeted, tailored, appropriate and acceptable hygiene and distancing measures, specifically for vulnerable groups and institutions, should be devised and their effect investigated.

From more testing to smart testing: data-guided SARS-CoV-2 testing choices, the Netherlands, May to September 2020.

BackgroundSARS-CoV-2 RT-PCR assays are more sensitive than rapid antigen detection assays (RDT) and can detect viral RNA even after an individual is no longer infectious. RDT can reduce the time to test and the results might better correlate with infectiousness.AimWe assessed the ability of five RDT to identify infectious COVID-19 cases and systematically recorded the turnaround time of RT-PCR testing.MethodsSensitivity of RDT was determined using a serially diluted SARS-CoV-2 stock with known viral RNA concentration. The probability of detecting infectious virus at a given viral load was calculated using logistic regression of viral RNA concentration and matched culture results of 78 specimens from randomly selected non-hospitalised cases. The probability of each RDT to detect infectious cases was calculated as the sum of the projected probabilities for viral isolation success for every viral RNA load found at the time of diagnosis in 1,739 confirmed non-hospitalised COVID-19 cases.ResultsThe distribution of quantification cycle values and estimated RNA loads for patients reporting to drive-through testing was skewed to high RNA loads. With the most sensitive RDT (Abbott and SD Biosensor), 97.30% (range: 88.65-99.77) of infectious individuals would be detected. This decreased to 92.73% (range: 60.30-99.77) for Coris BioConcept and GenBody, and 75.53% (range: 17.55-99.77) for RapiGEN. Only 32.9% of RT-PCR results were available on the same day as specimen collection.ConclusionThe most sensitive RDT detected infectious COVID-19 cases with high sensitivity and may considerably improve containment through more rapid isolation and contact tracing.

Supplementing SARS-CoV-2 genomic surveillance with PCR-based variant detection for real-time actionable information, the Netherlands, June to July 2021.

We evaluated routine testing with SARS-CoV-2 Delta variant-specific RT-PCR in regional hospital laboratories in addition to centralised national genomic surveillance in the Netherlands during June and July 2021. The increase of the Delta variant detected by RT-PCR correlated well with data from genomic surveillance and was available ca 2 weeks earlier. This rapid identification of the relative abundance and increase of SARS-CoV-2 variants of concern may have important benefits for implementation of local public health measures.

Unraveling the Modes of Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) During a Nursing Home Outbreak: Looking Beyond the Church Superspreading Event.

BACKGROUND: An outbreak of coronavirus disease 2019 (COVID-19) in a nursing home in the Netherlands, following an on-site church service held on 8 March 2020, triggered an investigation to unravel sources and chain(s) of transmission. METHODS: Epidemiological data were collected from registries and through a questionnaire among church attendees. Symptomatic residents and healthcare workers (HCWs) were tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by reverse-transcription polymerase chain reaction and subjected to whole genome sequencing (WGS). Sequences from a selection of people from the same area were included as community reference. RESULTS: After the church service, 30 of 39 attendees (77%) developed symptoms; 14 (11 residents and 3 nonresidents) were tested and were positive for COVID-19. In the following 5 weeks, 62 of 300 residents (21%) and 30 of 640 HCWs (5%) tested positive for COVID-19; 21 of 62 residents (34%) died. The outbreak was controlled through a cascade of measures. WGS of samples from residents and HCWs identified a diversity of sequence types, grouped into 8 clusters. Seven resident church attendees all were infected with distinct viruses, 4 of which belonged to 2 larger clusters in the nursing home. CONCLUSIONS: Although initial investigation suggested the church service as the source of the outbreak, detailed analysis showed a more complex picture, most consistent with widespread regional circulation of the virus in the weeks before the outbreak, and multiple introductions into the nursing home before the visitor ban. The findings underscore the importance of careful outbreak investigations to understand SARS-CoV-2 transmission to develop evidence-based mitigation measures.

Outbreak of COVID-19 on an industrial ship.

BACKGROUND: People on ships are at high risk for outbreaks of infectious diseases including coronavirus disease 2019 (COVID-19). A rapid and well-coordinated response is important to curb transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We studied an outbreak on an industrial ship to improve outbreak control for ships and coordination between participating harbour partners. MATERIALS AND METHODS: Public Health Service (PHS) Rotterdam-Rijnmond performed an epidemiological investigation during the outbreak of COVID-19 among 77 seafarers on a ship in their port. The captain was interviewed about ship details and his experiences during the outbreak. The seafarers were asked to fill in questionnaires about symptoms suspicious of COVID-19 and date of symptom onset. Information about stakeholders involved in outbreak control was registered. RESULTS: The captain first contacted PHS about probable cases on March 31st 2020 via a physician ashore. One crewmember was hospitalised on April 8th and another died unexpectedly aboard on April 10th. Questionnaires distributed mid-April to the 75 remaining seafarers showed that 38 of 60 responders (63%) had had suspicious symptoms between February 15th and April 13th. None of them were tested but a total of 8 other crewmembers tested positive for COVID-19 after leaving the ship, including the hospitalised crewmember and the one who died aboard. On May 5th, the last case left isolation and the quarantine ended. Many different stakeholders were involved in the outbreak response and responsibilities were not always fully clear beforehand, causing coordination issues. CONCLUSIONS: Testing crew with COVID-19 symptoms underpins control measures and clarifies communication between stakeholders. Building a network beforehand to develop outbreak guidelines tailored to ships and local circumstances is essential to control future outbreaks on ships.

A mixed-methods approach to elucidate SARS-CoV-2 transmission routes and clustering in outbreaks in native workers and labour migrants in the fruit and vegetable packaging industry in South Holland, the Netherlands, May to July 2020.

OBJECTIVES: To obtain insight into SARS-CoV-2 clustering and transmission routes during outbreaks in the predominantly migrant workforce of the fruit and vegetable packaging industry of South Holland, the Netherlands, May to July 2020. DESIGN: This mixed-methods study applied direct observation and interviews, epidemiologic investigation, source and contact data analysis and whole-genome sequencing. RESULTS: We detected 46 SARS-CoV-2 cases and 4 outbreaks with a proportional representation of labour migrant and native workers in 6 unrelated facilities. Complete viral genome sequences revealed at least 3 clusters of native workers and labour migrants, 2 within and 1 between facilities. On-site inspections found adequate implementation of preventative measures to which both native workers and labour migrants showed suboptimal adherence. Being a labour migrant was associated with living in shared housing, but not with more contacts or different sources. CONCLUSIONS: The fruit and vegetable packaging industry gave the impression of sufficient preparedness and control. Suboptimal adherence to the facilities' preventative guidelines could have facilitated work floor transmission. Community and household transmission are likely to have contributed to outbreaks. We encourage further research into risk factors for transmission in labour migrants and application of these insights into targeted public health policy.